Controllable lossy compression of BAM/CRAM files
meta
Groovy Map containing sample information e.g. [ id:‘test’, single_end
input
BAM/CRAM/SAM file
*.{bam,cram,sam}
keepbed
BED file defining regions to keep quality
bedout
set to true to ouput suspicious regions to a BED file
versions
File containing software versions
versions.yml
bam
optional filtered/compressed BAM file
*.{bam}
cram
optional filtered/compressed CRAM file
*.{cram}
sam
optional filtered/compressed SAM file
*.{sam}
bed
optional suspicious regions BED file
*{bed}
